Run python script after transforms
you could use a python script that runs through all your objects and checks if their scale is 1,1,1 and rotation is 0°,0°,0°. if not it applies rotation&amp;scale

import bpy

for obj in  bpy.context.scene.objects:
    if obj.scale!=[1,1,1] or obj.rotation_euler!=[0,0,0] :
        bpy.context.scene.objects.active=obj
        bpy.ops.object.transform_apply(location=False, rotation=True, scale=True)